EuroPneumo Special Issue / pneumonia 2015 Oct 21;7:I–72


Genome-wide assessment of pneumococcal antigenic diversity

Nicholas Croucher 1 , Lisa Kagedan 2 , Claudette Thompson 2 , Julian Parkhill 3 , Stephen Bentley 3 ,

Jonathan Finkelstein 4 , Marc Lipsitch 2 , William Hanage 2


Imperial College, London, UK; 2 Harvard School of Public Health, Boston, USA, 3 Wellcome Trust Sanger Institute, Cambridge, UK, 4 Harvard Medical

School, Boston, USA

Extensive variation in both polysaccharide and protein antigens is evident across pneumococcal populations. The

variation in these surface structures can be quantified through whole genome sequencing of systematic samples of

pneumococci isolated from carriage. Data from 616 isolates collected in Massachusetts between 2001 and 2007 allowed

characterisation of 20 serotype switching events. These revealed a highly significant (p < 0.0001) enrichment for withinserogroup

switching, based on the observed serotype distribution. However, this pattern could not be fully explained by

more frequent, shorter recombinations preferentially driving the smaller changes required to switch between serotypes

of the same serogroup. Although a separate dataset indicated vaccine escape sometimes associated with changes in

β–lactam resistance, the pattern of switching in this collection was not detectably affected by linkage between pbp

genes and the capsule polysaccharide synthesis (cps) locus. The absence of an explanation based on the properties

of transformation suggested the observed pattern was a consequence of selection for preserving serogroup. Hence

multiple exchanges of serotypes were experimentally constructed in common genetic backgrounds to test for epistatic

interactions between the cps locus and other pneumococcal genes. However, these data were not consistent with

epistatic interactions between cps loci of a particular serogroup and the rest of the genome, meaning they were unlikely

to account for the observed distribution of capsule types. These data suggested future work should focus on alternative

mechanisms, such as host immunity spanning multiple serotypes within the same serogroups, which might explain this

significant trend. Characterisation of proteinaceous antigens found them to be highly diverse across the population.

However, individual alleles were stably associated with particular lineages, with only pspA and pspC undergoing

diversification over short timescales. Together, these data show how individual lineages are likely to be restricted in how

they diversify under host immune selection pressure.


An increase in negative supercoiling in Streptococcus pneumoniae

induces a global transcriptomic response that regulates the DNA

topoisomerase I gene

Maria-José Ferrándiz 1 , Antonio-Javier Martín-Galiano 1 , Isabel Camacho-Soguero 1 , Cristina

Arnanz 1 , Adela G. de la Campa 1, 2


Centro Nacional de Microbiología, ISCIII and CIBERES, Majadahonda/ Madrid, Spain; 2 Presidencia. CSIC, Madrid, Spain

The most basic level of transcription regulation in Streptococcus pneumoniae results from the organisation of its

chromosome into topological domains. We have previously observed a global transcriptional response to DNArelaxation.

In this study, to increase DNA supercoiling, we used seconeolitsine (SCN), an inhibitor of topoisomerase I.

Supercoiling density (σ) varied as a function of time as a result of treatment with SCN at 0.5 × MIC: 48%, 74%, and 46%

at 5 min, 15 min and 30 min of treatment, respectively. A global transcriptomic response was observed. The number

of responsive genes decreased from a high 395 at 5 min to 285 at 15 min, to 150 at 30 min (a drop of more than half).

More than one-third of the responsive genes at 15 min were found to be contiguous in the chromosome, forming

clusters that showed coordinated regulation. At least 10 clusters were discerned. Clusters were evident at 5 and 15

min. The only DNA topoisomerase gene significantly affected was topA, which was 3-fold down-regulated at 15 min.

After 30 min, topA transcripts were restored to baseline levels, coincident with partial recovery of the supercoiling and

reduction of the transcriptomic response. For the first time here, we have identified in bacteria, the existence of a global

transcriptomic response triggered by an increase in DNA supercoiling. This response is similar to the one observed

during DNA relaxation. This indicates that they are handled globally as a common type of topological stress.

pneumonia 2015 Volume 7


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